How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools

Question

[hashim.rana11]

. I am using mtDNA PacBio data to calculate nucleotide diversity. For my analysis, I have been utilizing bioinformatics tools on a Linux platform. Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity, but I was unsuccessful. Suggest me some tools for these calculations. I humbly request your guidance from the beginning. Could please someone help me?

Thank you for your assistance.

Best regards,

[Pierre Lindenbaum]

, but I was unsuccessful.

what does it mean ?

[hashim.rana11]

Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity

Answer 1

[Michael]

Variants should be called using a specialized mitochondrial variant caller, e.g.: GATK Mutect2 CallMt

Then, pi, Tajima's D, and other statistics could be estimated with vcftools from the vcf files, here is a tutorial.